Scn plants and methods for making the same

ABSTRACT

The invention relates to genes which may be utilized for resistance to soybean cyst nematode. More specifically the present disclosure relates to identification of gene(s) that can confer upon a soybean plant resistance to soybean cyst nematode (SCN) and methods to use these loci and genes to obtain soybean strains that are resistant to SCN.

CROSS-REFERENCE TO RELATED APPLICATION

This application claims the benefit of U.S. Provisional Application Ser.No. 62/099,035, filed Dec. 31, 2014, the disclosure of which is herebyincorporated by reference in its entirety, including all figures, tablesand amino acid or nucleic acid sequences.

The Sequence Listing for this application is labeled “Seq-List.txt”which was created on Dec. 24, 2015 and is 961 KB. The entire contents ofthe sequence listing is incorporated herein by reference in itsentirety.

FIELD OF THE INVENTION

This invention relates to genes which may be utilized for resistance tosoybean cyst nematode. More specifically the present disclosure relatesto identification of gene(s) that can confer upon a soybean plantresistance to soybean cyst nematode (SCN) and methods to use these lociand genes to obtain soybean strains that are resistant to SCN.

BACKGROUND OF THE INVENTION

Soybeans (Glycine max) are a major cash crop and investment commodityaround the world. Soybean oil is one of the most widely used edibleoils, and soybeans themselves are used worldwide both in animal feed andin human food production.

Soybean cyst nematode (SCN) causes substantial yield loss in NorthAmerican soybean. Heterodera glycines Ichinohe, was first identified onsoybeans in the United States in 1954 at Castle Hayne, N. C. Winstead,et al., Plant Dis. Rep. 39:9-11, 1955. Since its discovery the soybeancyst nematode (“SCN”) has been recognized as one of the most destructivepests in soybean in the United States and worldwide. It has beenreported in nearly all states in which soybeans are grown, and it causesmajor production problems in several states, being particularlydestructive in the midwestern states. See generally: Calwell, et al.,Agron. J. 52:635-636, 1960; Rao-Arelli and Anand, Crop. Sci. 28:650-652,1988; Baltazar and Mansur, Soybean Genet. Newsl. 19:120-122, 1992;Concibido, et al., Crop. Sci., 1993. For example, susceptible soybeancultivars had 6-36% lower seed yields than did resistant cultivars onSCN race-3 infested sites in Iowa (Niblack and Norton 1992). Since thediscovery of SCN in the United States in the 1970s, extensive effortshave been made to identify new SCN resistance sources by screeningGlycine max plant introductions (PIs) of the USDA soybean germplasmcollection (Anand et al. 1988; Arelli et al. 2000; Arelli et al. 1997;Young 1995). Chen et al. (2006) used bioassay to characterize over 120SCN resistance soybean accessions with SCN races 3, -5, and -14 andreported many PIs including PI 437654, PI 438489B, PI 90763, PI 89772,PI 404198A, and PI 567516C with high resistance levels to multi-races.

Although several SCN resistance quantitative trait loci (QTLs) have beendiscovered in PI 437654 (Concibido et al., 2004, U.S. Pat. No. 6,096,944issued to Vierling et al. and U.S. Pat. No. 6,538,175 issued to Webb),many SCN resistance QTLs remain to be identified. More SCN sources ofresistance have been evaluated extensively to identify novel QTLs andepistatic effects between QTLs (Wu et al 2009). Among soybean PIsevaluated for SCN resistance, PI 437654, PI 467312, PI 438489B, and PI567516C have been reported to be highly resistant to multi-races (alsoknown as HG types) of SCN. In addition, PI 567516C is also resistant toa synthetic nematode population LY1 and genetically unique from mostother SCN resistant sources, including Peking and PI 88788 that arewidely used in current SCN resistant varieties.

SCN accounts for roughly 40% of the total disease in soybean and canresult in significant yield losses (up to 90%). SCN is the mostdestructive pest of soybean to date and accounts for an estimated yieldloss of up to $1 billion dollars annually. Currently, the most costeffective control measures are crop rotation and the use of host plantresistance. While breeders have successfully developed SCN resistantsoybean lines, breeding is both difficult and time consuming due to thecomplex and polygenic nature of resistance. The resistance is often racespecific and does not provide stability over time due to changing SCNpopulations in the field. In addition, many of the resistant soybeanvarieties carry a significant yield penalty when grown in the absence ofSCN.

Although the use of nematocides is effective in reducing the populationlevel of the nematode, nematocide use is both uneconomical andpotentially environmentally unsound as a control measure in soybeanproduction. Neither is crop rotation a practical means of nematodecontrol, since rotation with a nonsusceptible crop for at least twoyears is necessary for reducing soybean losses. Therefore, it has longbeen felt by soybean breeders that use of resistant varieties is themost practical control measure.

Screening of soybean germplasm for resistance to SCN was begun soonafter the discovery of the nematode in the United States, and Golden, etal. (Plant Dis. Rep. 54:544-546, 1970) have described the determinationof SCN races. Although SCN was discovered in North America about 40years ago, soybean breeding for resistance to SCN has mostly utilizedgenes from two plant introductions—Peking and PI88788, and while theselines have resistance genes for several SCN races, including race-3,they do not provide resistance to all known races.

The plant introduction PI 437.654 is the only known soybean to haveresistance to SCN races-3 (Anand 1984) (Anand 1985) and (Rao-Arelli etal. 1992b). However, PI 437.654 has a black seed coat, poorstandability, seed shattering, and low yield, necessitating theintrogression of its SCN resistance into elite germplasm with a minimumof linkage drag. Conventional breeding with PI 437.654 produced thevariety ‘Hartwig’ (Anand 1991), which is more adapted to cultivation andcan be used as an alternative source of SCN resistance in soybeanbreeding programs.

Resistance to SCN is multigenic and quantitative in soybean (Mansur etal. 1993), though complete resistance can be scored qualitatively. Forcomplete resistance to SCN, PI 437.654 has two or three loci for race-3,two or four loci for race-5, and three or four loci for race-14 (Myersand Anand 1991). The multiple genes and SCN races involved contribute tothe difficulty breeders have in developing SCN resistant soybeanvarieties.

Breeding programs for SCN resistance rely primarily on field evaluationswhere natural nematode populations occur. However, these populations canbe mixtures of undetermined races (Young 1982) and the environment canaffect the overwintering and infection capability of the nematodes(Niblack and Norton 1992). Although evaluations using inbred nematodepopulations in controlled greenhouse environments are superior, they areprohibitively expensive and the nematodes are difficult to manage forlarge breeding programs (Rao-Arelli, pers comm). These deficiencies ineach evaluation method make SCN resistance a difficult trait tomanipulate in soybean improvement programs. Host plant resistance is aneffective approach to control this pest; however, continuously growingthe same resistant cultivar(s) may result in SCN population shifts andloss of SCN resistant phenotype.

Therefore, discovery of new sources of genetic resistance is fullywarranted.

SUMMARY OF THE INVENTION

The present invention includes methods for detecting SCN resistance in aplant, comprising the steps of: (a) measuring expression level of a genein a sample taken from the subject, and (b) comparing the expressionlevel obtained in step (a) with a standard control, wherein a decreasein the expression level of the gene when compared with the standardcontrol indicates the plant has SCN resistance. Such methods can includesyncytium regulated genes or miRNA genes.

Additional embodiments of the invention can include methods fordetecting SCN resistance in a plant, comprising the steps of: (a)treating a sample taken from the subject with an agent thatdifferentially modifies methylated and demethylated DNA; and (b)determining whether each CpG in a CpG-containing genomic sequence ismethylated, demethylated and/or hypomethylated, wherein presence of onemethylated CpG in the CpG-containing genomic sequence indicates thesubject having increased SCN resistance. The CpG-containing genomicsequences can comprise one or more CpG containing sequences.

Other embodiments include methods for detecting SCN resistance in aplant, comprising the steps of: (a) treating a sample taken from thesubject with an agent that differentially modifies methylated,demethylated and/or hypomethylated DNA; and (b) determining whether eachCHG in a CHG-containing genomic sequence is methylated, demethylatedand/or hypomethylated, wherein presence of one methylated CHG in theCHG-containing genomic sequence indicates the subject having increasedSCN resistance.

Embodiments can also include methods for detecting SCN resistance in aplant, comprising the steps of: (a) treating a sample taken from thesubject with an agent that differentially modifies methylated,demethylated and/or hypomethylated DNA; and (b) determining whether eachCHH in a CHH-containing genomic sequence is methylated, demethylatedand/or hypomethylated, wherein presence of one methylated CHH in theCHH-containing genomic sequence indicates the subject having increasedSCN resistance. The present invention also includes elite soybeanplants, or a part thereof, comprising one or more introgressed SoybeanCyst Nematode (SCN) resistance loci, wherein said elite soybean plantcomprises one or more agronomic traits selected from the groupconsisting of herbicide tolerance, increased yield, insect control,fungal disease resistance, virus resistance, nematode resistance,bacterial disease resistance, mycoplasma disease resistance, modifiedoils production, high oil production, high protein production,germination and seedling growth control, enhanced animal and humannutrition, lower raffinose, environmental stress resistance, increaseddigestibility, production of industrial enzymes, production ofpharmaceutical proteins, production of pharmaceutical peptides,production of pharmaceutical small molecules, improved processingtraits, improved flavor, improved nitrogen fixation, improved hybridseed production, reduced allergenicity, and improved production ofbiopolymers and biofuels. The elite soybean plant can be resistant toHeterodera glycines. In various embodiments, the elite soybean plant, orpart thereof, of comprises one or more heterologous nucleic acidsequences encoding one or more miRNA selected from SEQ ID NOs: 1-37 oneor more constructs comprising a heterologous promoter operably linked toa nucleic acid sequence encoding one or more miRNA selected from SEQ IDNOs: 1-37. Yet other embodiments provide an elite soybean plant thatcomprises one or more heterologous nucleic acid sequences encoding oneor more gene selected from SEQ ID NOs: 38-315 or one or more constructcomprising a heterologous promoter operably linked to a nucleic acidsequence encoding one or more gene selected from SEQ ID NOs: 38-315.Still other embodiments provide an elite soybean plant comprises one ormore heterologous nucleic acid sequences encoding one or more miRNAselected from SEQ ID NOs: 1-37 and one or more heterologous nucleic acidsequences encoding one or more gene selected from SEQ ID NOs: 38-315 orone or more constructs comprising a heterologous promoter operablylinked to a nucleic acid sequence encoding one or more miRNA selectedfrom SEQ ID NOs: 1-37 and one or more construct comprising aheterologous promoter operably linked to a nucleic acid sequenceencoding one or more gene selected from SEQ ID NOs: 38-315.

Additional methods of the present invention include methods of selectingat least one soybean plant by marker assisted selection of aquantitative trait locus (“QTL”) associated with soybean cyst nematoderesistance, wherein said QTL is localized to a chromosomal interval,said method comprising testing at least one marker on said chromosomalinterval for said QTL and selecting said soybean plant comprising saidQTL. The selected soybean plant can be used in a cross to introgresssaid QTL into progeny soybean germplasm.

Other embodiments of the present invention can include methods forgenerating a soybean plant, said methods comprising (a) introgressingSCN resistance into an SCN sensitive soybean germplasm, (b) determiningthe presence or absence of a marker gene or a fragment thereof and atransgene, said marker gene being selected from the group consisting ofthe polynucleotide molecules of specific sequences and (c) allowing thegermplasm generated in (a) to develop into a soybean plant resistant tosoybean cyst nematode (SCN) if the marker and transgene are present,wherein step (a) precedes step (b). In various embodiments, the soybeanplant is introgressed to contain one or more heterologous nucleic acidsequences encoding one or more miRNA selected from SEQ ID NOs: 1-37 orone or more constructs comprising a heterologous promoter operablylinked to a nucleic acid sequence encoding a miRNA selected from SEQ IDNOs: 1-37. Yet other embodiments provide a soybean plant that isintrogressed to contain one or more heterologous nucleic acid sequencesencoding one or more gene selected from SEQ ID NOs: 38-315 or one ormore construct comprising a heterologous promoter operably linked to anucleic acid sequence encoding one or more gene selected from SEQ IDNOs: 38-315. Still other embodiments provide a soybean plant that isintrogressed to contain one or more heterologous nucleic acid sequencesencoding one or more miRNA selected from SEQ ID NOs: 1-37 and one ormore heterologous nucleic acid sequences encoding one or more geneselected from SEQ ID NOs: 38-315 or one or more construct comprising aheterologous promoter operably linked to a nucleic acid sequenceencoding one or more gene selected from SEQ ID NOs: 38-315 and one ormore constructs comprising a heterologous promoter operably linked to anucleic acid sequence encoding a miRNA selected from SEQ ID NOs: 1-37.

Additional embodiments of the present invention include methods ofselecting a population of plants or seeds with SCN resist comprising thesteps of: a) providing a population consisting of a plurality ofindividual plants which are genetically uniform; b) isolating a tissuesample or explant from individual plants of said population in a mannerwhich allows further cultivation of said sampled individual plants; c)determining the SCN resistance of said individual plants by analyzingsaid sample of said plants; d) selecting a number of plants wherein saidsample exhibits resistance to SCN from said population; e) growing theselected plants and propagating from each of the selected plants a lineof cloned progeny plants; f) determining the SCN resistance for eachline of cloned progeny plants; g) selecting a line of clone plantswherein said SCN resistance is higher than the average of the SCNresistance of all lines of cloned progeny plants; h) growing apopulation of individual plants from said selected line of clone progenyplants; and i) repeating at least once steps b to h on said subsequentpopulation. The SCN resistance can be determined by methods including a)determining the methylated regions in a plant; b) determining thehypo-methylated and hyper-methylated regions in a CpG, CHG or CHHcontext; c) comparing methylation levels of the genes in the syncytiumto determine the SCN resistance potential of a plant.

Embodiments of the present invention also include methods for producingan SCN resistant soybean plant comprising: a. performing marker assistedselection to identify a soybean plant possessing a resistance allele ofSCN resistance locus, wherein the SCN resistance locus is identifiableby one or more of the markers and generating a progeny of said soybeanplant wherein said progeny possesses said resistance allele of SCNresistance locus and exhibits at least partial resistance to SCN. Suchmethods can comprise soybean plants that further comprise one or moretraits selected from the group consisting of herbicide tolerance,increased yield, insect control, fungal disease resistance, virusresistance, nematode resistance, bacterial disease resistance,mycoplasma disease resistance, modified oils production, high oilproduction, high protein production, germination and seedling growthcontrol, enhanced animal and human nutrition, lower raffinose,environmental stress resistance, increased digestibility, improvedprocessing traits, improved flavor, improved nitrogen fixation, improvedhybrid seed production, reduced allergenicity, and improved productionof biofuels.

The present invention can additionally include methods for generating atransgenic plant using a host plant, said transgenic plant being moreresistant to soybean cyst nematode (SCN) when compared to the hostplant, said method comprising a step of introducing at least onetransgene into said host plant, said at least one transgene beinglocated within the chromosomal region. In various embodiments, thetransgene comprises one or more heterologous nucleic acid sequencesencoding one or more miRNA selected from SEQ ID NOs: 1-37. In yet otherembodiments, the transgene comprises one or more heterologous nucleicacid sequences encoding one or more gene selected from SEQ ID NOs:38-315. In still other embodiments, the transgene comprises one or moreheterologous nucleic acid sequences encoding one or more miRNA selectedfrom SEQ ID NOs: 1-37 and one or more heterologous nucleic acidsequences encoding one or more gene selected from SEQ ID NOs: 38-315. Asused within this application, the phrase “heterologous nucleic acid”(and variations of this phrase) is used to indicate that the soybeanplant into which one or more of SEQ ID NOs: 1-315 are introduced (byintrogression or transformation for example) is not found within thegenome of the soybean plant that was transformed or introgressed or thatthe soybean plant has been transformed or introgressed with one or moreof SEQ ID NOs: 1-315 operably linked to a heterologous promoter (i.e.,the promoter operably linked to any one or more of SEQ ID NOs: 1-315 isnot the native promoter associated with the nucleic acid sequence of SEQI NOs: 1-315). Such heterologous promoters are discussed below andinclude, but are not limited to, constitutive, inducible and tissuespecific (preferred) promoters. A nucleic acid sequence that comprises aheterologous promoter operably linked to any one of SEQ ID NOs: 1-315may be referred to as a “construct” within this application.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a number of differentially hyper- and hypo-methylated regionin response to SCN infection.

FIG. 2A is a venn diagram showing genes that are hyper-methylated invarious contexts. FIG. 2B is a venn diagram showing genes that arehypo-methylated in various contexts.

FIG. 3A is a bar chart illustrating the distribution of differentiallyhyper-methylated regions in various features of protein-coding genes.FIG. 3B is a bar chart illustrating the distribution of differentiallyHypo-methylated regions in various features of protein-coding genes.

FIG. 4A illustrates the Gene Ontology categorization of the molecularfunctions of the differentially methylated genes. FIG. 4B illustratesthe Gene Ontology categorization of the biological processes of thedifferentially methylated genes.

FIGS. 5A-5D depict the functional classification of differentiallymethylated genes overlapping with syncytium differentially expressedgenes. A and B: Venn diagrams showing overlaps between differentiallyhyper-methylated (A) and Hypo-methylated (B) genes with syncytiumdifferentially expressed genes. C and D; Gene Ontology categorization ofthe molecular functions (C) or the biological processes (D) of thedifferentially methylated genes overlapping with syncytiumdifferentially expressed genes.

FIGS. 6A-6D illustrate quantitative real-time RT-PCR (qPCR) assaysshowing the impact of differential hyper- and hypo-methylation on geneexpression levels.

DETAILED DESCRIPTION OF THE EMBODIMENTS OF THE INVENTION

The present invention relates to a novel and useful method forintrogressing, in a reliable and predictable manner, SCN resistance intonon-resistant soybean germplasm. The method involves the genetic-mappingof loci associated with SCN resistance. SCN race resistance can bedetermined in any acceptable manner; preferably in greenhouse conditionsusing a homogenous population of the particular SCN race.

Embodiments of the present inventions including studies on epigeneticmodifications function in concert with genetic mechanisms to regulatetranscriptional activity in normal cells and are often disregulated ininfected cells. Epigenomics is the study of the pattern of chemicalmarkers that serve as a regulatory layer on top of the DNA sequence.Depending on where they grow, the plants' epigenomic differences mayallow them to rapidly adapt to their environments. Epigenomicmodifications alter gene expression without changing the letters of theDNA alphabet (A-T-C-G), providing cells with an additional tool tofine-tune how genes control the cellular machinery.

By understanding epigenomic alterations in plants, the present inventioncan manipulate such alterations for various purposes, including biofuelsand creating crops that can withstand stressful events such as drought.Such knowledge of epigenomic changes in crop plants could tell producerswhat to breed for and could have a huge impact on identifying plantsthat can survive certain conditions and adapt to environmental stresses.In the present invention such knowledge relates to SCN resistance.

Epigenetics can be defined as the biochemical modifications of DNA andassociated proteins that regulate gene expression and chromosomestructure and function, without changing DNA nucleotide sequences. DNAmethylation, the most common epigenetic modifications, is the additionor removal of a methyl group (CH₃), mostly where cytosine bases occurrepeatedly. In plants, DNA methylation occurs in symmetric (CG and CHG)and asymmetric (CHH) contexts where H refers to any nucleotide but G.The CG and CHG patterns are symmetric across the two DNA strands, whichare believed to be important for the maintenance of methylation at thesesites following DNA replication. DNA cytosine methylation, as the mainepigenetic mark, controls gene expression networks and hence playsessential roles in different aspects of plant growth, development, andresponse to biotic stress (Zhang et al., 2010; He et al., 2011, Dowen etal. 2012). While DNA methylation has been initially reported to controlvarious developmental processes in plants, recent studies revealed thatthis silencing pathway plays a key role in modulating plant defenseresponses during biotrophic interactions (Yu et al., 2013; Dowen et al.2012; Luna et al., 2012). Recently, Dowen et al. (2012) provided a clearevidence of dynamic changes in DNA methylation in response to infectionby the bacterial pathogen Pseudomonas syringae pv. tomato DC3000 (Pst).Using deep sequencing of bisulfite treated DNA, they found thatdifferentially methylated regions (DMRs) are preferentially associatedwith genes involved in defense response, and that hypomethylation inDMRs is frequently accompanied by activation of the proximal genes,specifically those with defense response function. Similarly, anotherrecent study indicated that DNA demethylation restricts themultiplication and vascular propagation of the Pst and, consequentlysome immune response genes, are repressed by DNA methylation (Yu et al.,2013). Chemical demethylation of the silenced resistance Xa21G gene inrice reestablished its resistance function against Xanthomomonas oryzae(Akimoto et al., 2007). Similarly, induced DNA hypomethylation at theNBS-LRR gene clusters by the tobacco mosaic virus was associated withincreased genomic rearrangements at these genomic loci (Boyko et al.,2007). The expression difference between the resistant alleles of theMedicago truncatula REP1 gene, which confers resistance against thepowdery mildew disease caused by the biotrophic fungus Erysiphe pisi,was found to be correlated with the methylation status at the promoterregions (Yang et al., 2013). In soybean, differential hypermethylationpatterns at the genomic regions that contain multiple copies of SCNresistance gene Rhg1 have been recently identified (Cook et al., 2014).Collectively these results indicate that DNA methylation plays a crucialrole in regulating the immune system in response to pathogen infectionincluding cyst nematodes.

Epigenetic variation is when the phenotypic traits of an individual varywithout altering the primary sequence of its DNA. This can occur throughchanges in the expression of particular genes via processes such as DNAmethylation and chromatin remodelling, and by influencing the activityof RNA structures which regulate levels of gene expression.

Epigenetic changes in gene expression enable an individual to respond tochanges in the environment and adjust the synthesis of proteinsaccordingly. It has become apparent that while many of the epigeneticmodifications to the genome are reset during the process of meiosis,some epigenetic information can be transmitted between generations, sothat the phenotypic traits of offspring are affected without alteringthe primary structure of the DNA. Thus offspring can inherit toleranceto a particular environmental condition before they have been exposed.

A nucleotide segment is referred to as “operably linked” when it isplaced into a functional relationship with another DNA segment (forexample, a promoter that is operably linked to any one of SEQ ID NOs:1-315). However, enhancers need not be contiguous with the codingsequences whose transcription they control. Linking is accomplished byligation at convenient restriction sites or at adapters or linkersinserted in lieu thereof. The expression cassette can include one ormore enhancers in addition to the promoter. By “enhancer” is intended acis-acting sequence that increases the utilization of a promoter. Suchenhancers can be native to a gene or from a heterologous gene. Further,it is recognized that some promoters can contain one or more native,enhancers or enhancer-like elements. An example of one such enhancer isthe 35S enhancer, which can be a single enhancer, or duplicated. See forexample, McPherson et al, U.S. Pat. No. 5,322,938, which is herebyincorporated by reference in its entirety.

The promoter for driving expression of the transgenic polynucleotide ofinterest may be selected based on a number of criteria including, butnot limited to, what the desired use is for the operably linkedpolynucleotide, what location in the plant is expression of thetransgenic polynucleotide of interest desired, and at what level isexpression of transgenic polynucleotide of interest desired or whetherit needs to be controlled in another spatial or temporal manner. In oneaspect, a promoter that directs expression to particular tissue may bedesirable. When referring to a promoter that directs expression to aparticular tissue is meant to include promoters referred to as tissuespecific or tissue preferred. Included within the scope of the inventionare promoters that express highly in the plant tissue, express more inthe plant tissue than in other plant tissue, or express exclusively inthe plant tissue. For example, “seed-specific” promoters may be employedto drive expression. Specific-seed promoters include those promotersactive during seed development, promoters active during seedgermination, and/or that are expressed only in the seed. Seed-specificpromoters, such as annexin, P34, beta-phaseolin, alpha subunit ofbeta-conglycinin, oleosin, zein, napin promoters have been identified inmany plant species such as maize, wheat, rice and barley. See U.S. Pat.Nos. 7,157,629, 7,129,089, and 7,109,392. Such seed-preferred promotersfurther include, but are not limited to, Cim1 (cytokinin-inducedmessage); cZ19B1 (maize 19 kDa zein); and milps(myo-inositol-1-phosphate synthase); (see WO 00/11177, hereinincorporated by reference). The 27 kDa gamma-zein promoter is apreferred endosperm-specific promoter. The maize globulin-1 and oleosinpromoters are preferred embryo-specific promoters. For dicots,seed-specific promoters include, but are not limited to, bean betaphaseolin, napin, beta-conglycinin, soybean lectin, cruciferin, and thelike. For monocots, seed-specific promoters include, but are not limitedto, promoters of the 15 kDa beta-zein, 22 kDa alpha-zein, 27 kDagamma-zein, waxy, shrunken 1, shrunken 2, globulin 1, an Ltp1, an Ltp2,and oleosin genes. See also WO 00/12733, where seed-preferred promotersfrom end1 and end2 genes are disclosed; herein incorporated byreference. Each of these aforementioned references are herebyincorporated by reference in their entireties, particularly as relatesto the promoters disclosed within the references.

The promoters useful in the present invention can also includeconstitutive, inducible or tissue-specific (preferred) promoters thatare operably linked to any one of SEQ ID NOs: 1-315 and are heterologousto the nucleic acid sequences to which they are operably linked. Inother words, the promoters are not those found operably linked to anyone of the nucleic acid sequence encoding the genes or miRNA of SEQ IDNOs: 1-315 in their native context within a soybean plant. Constitutivepromoters, generally, are active in most or all tissues of a plant;inducible promoters, which generally are inactive or exhibit a low basallevel of expression, and can be induced to a relatively high activityupon contact of cells with an appropriate inducing agent;tissue-specific (or tissue-preferred) promoters, which generally areexpressed in only one or a few particular cell types (e.g., root cells);and developmental-or stage-specific promoters, which are active onlyduring a defined period during the growth or development of a plant.Often promoters can be modified, if necessary, to vary the expressionlevel. Certain embodiments comprise promoters exogenous to the speciesbeing manipulated (e.g. a soybean plant).

Non-limiting examples of root-specific promoters (a subset oftissue-specific promoters) include root preferred promoters, such as themaize NAS2 promoter, the maize Cyclo promoter (US 2006/0156439,published Jul. 13, 2006), the maize ROOTMET2 promoter (WO05063998,published Jul. 14, 2005), the CR1BIO promoter (WO06055487, published May26, 2006), the CRWAQ81 (WO05035770, published Apr. 21, 2005) and themaize ZRP2.47 promoter (NCBI accession number: U38790; GI No. 1063664).Each of these aforementioned references are hereby incorporated byreference in their entireties, particularly as relates to the promotersdisclosed within the references.

Exemplary constitutive promoters include the 35S cauliflower mosaicvirus (CaMV) promoter (Odell et al. (1985) Nature 313:810-812), themaize ubiquitin promoter (Christensen et al. (1989) Plant Mol. Biol.12:619-632 and Christensen et al. (1992) Plant Mol. Biol. 18:675-689);the core promoter of the Rsyn7 promoter and other constitutive promotersdisclosed in WO 99/43838 and U.S. Pat. No. 6,072,050; rice actin(McElroy et al. (1990) Plant Cell 2:163-171); pEMU (Last et al. (1991)Theor. Appl. Genet. 81:581-588); MAS (Velten et al. (1984) EMBO J.3:2723-2730); ALS promoter (U.S. Pat. No. 5,659,026); rice actinpromoter (U.S. Pat. No. 5,641,876; WO 00/70067), maize histone promoter(Brignon et al., Plant Mol Bio 22(6):1007-1015 (1993); Rasco-Gaunt etal., Plant Cell Rep. 21(6):569-576 (2003)) and the like. Otherconstitutive promoters include, for example, those described in U.S.Pat. Nos. 5,608,144 and 6,177,611, and PCT publication WO 03/102198.Each of these aforementioned references are hereby incorporated byreference in their entireties, particularly as relates to the promotersdisclosed within the references.

An inducible promoter/regulatory element is one that is capable ofdirectly or indirectly activating transcription of one or more of SEQ IDNOs: 1-315 in response to an inducer. The inducer can be a chemicalagent such as a protein, metabolite, growth regulator, herbicide orphenolic compound; or a physiological stress, such as that imposeddirectly by heat, cold, salt, or toxic elements, or indirectly throughthe action of a pathogen or disease agent such as a virus; or otherbiological or physical agent or environmental condition. A plant cellcontaining an inducible promoter/regulatory element may be exposed to aninducer by externally applying the inducer to the cell or plant such asby spraying, watering, heating or similar methods. An inducing agentuseful for inducing expression from an inducible promoter is selectedbased on the particular inducible regulatory element. In response toexposure to an inducing agent, transcription from the inducibleregulatory element generally is initiated de novo or is increased abovea basal or constitutive level of expression.

Any inducible promoter/regulatory element can be used in the instantinvention (See Ward et al., Plant Mol. Biol. 22: 361-366, 1993).Non-limiting examples of such promoters/regulatory elements include: ametallothionein regulatory element, a copper-inducible regulatoryelement, or a tetracycline-inducible regulatory element, thetranscription from which can be effected in response to divalent metalions, copper or tetracycline, respectively (Furst et al., Cell55:705-717, 1988; Mett et al., Proc. Natl. Acad. Sci., USA 90:4567-4571, 1993; Gatz et al., Plant J. 2:397-404, 1992; Roder et al., Mol.Gen. Genet. 243:32-38, 1994). Inducible promoters/regulatory elementsalso include an ecdysone regulatory element or a glucocorticoidregulatory element, the transcription from which can be effected inresponse to ecdysone or other steroid (Christopherson et al., Proc.Natl. Acad. Sci., USA 89:6314-6318, 1992; Schena et al., Proc. Natl.Acad. Sci., USA 88:10421-10425, 1991; U.S. Pat. No. 6,504,082); a coldresponsive regulatory element or a heat shock regulatory element, thetranscription of which can be effected in response to exposure to coldor heat, respectively (Takahashi et al., Plant Physiol. 99:383-390,1992); the promoter of the alcohol dehydrogenase gene (Gerlach et al.,PNAS USA 79:2981-2985 (1982); Walker et al., PNAS 84(19):6624-6628(1987)), inducible by anaerobic conditions; and the light-induciblepromoter derived from the pea rbcS gene or pea psaDb gene (Yamamoto etal. (1997) Plant J. 12(2):255-265); a light-inducible regulatory element(Feinbaum et al., Mol. Gen. Genet. 226:449, 1991; Lam and Chua, Science248:471, 1990; Matsuoka et al. (1993) Proc. Natl. Acad. Sci. USA90(20):9586-9590; Orozco et al. (1993) Plant Mol. Bio. 23(6):1129-1138), a plant hormone inducible regulatory element(Yamaguchi-Shinozaki et al., Plant Mol. Biol. 15:905, 1990; Kares etal., Plant Mol. Biol. 15:225, 1990), and the like. An induciblepromoter/regulatory element also can be the promoter of the maize In2-1or In2-2 gene, which responds to benzenesulfonamide herbicide safeners(Hershey et al., Mol. Gen. Gene. 227:229-237, 1991; Gatz et al., Mol.Gen. Genet. 243:32-38, 1994), and the Tet repressor of transposon Tn10(Gatz et al., Mol. Gen. Genet. 227:229-237, 1991). Stress induciblepromoters include salt/water stress-inducible promoters such as PSCS(Zang et al. (1997) Plant Sciences 129:81-89); cold-inducible promoters,such as, cor15a (Hajela et al. (1990) Plant Physiol. 93:1246-1252),cor15b (Wlihelm et al. (1993) Plant Mol Biol 23:1073-1077), wsc120(Ouellet et al. (1998) FEBS Lett. 423-324-328), ci7 (Kirch et al. (1997)Plant Mol Biol. 33:897-909), ci21A (Schneider et al. (1997) PlantPhysiol. 113:335-45); drought-inducible promoters, such as, Trg-31(Chaudhary et al (1996) Plant Mol. Biol. 30:1247-57), rd29 (Kasuga etal. (1999) Nature Biotechnology 18:287-291); osmotic induciblepromoters, such as Rab17 (Vilardell et al. (1991) Plant Mol. Biol.17:985-93) and osmotin (Raghothama et al. (1993) Plant Mol Biol23:1117-28); and heat inducible promoters, such as heat shock proteins(Barros et al. (1992) Plant Mol. 19:665-75; Marrs et al. (1993) Dev.Genet. 14:27-41), smHSP (Waters et al. (1996) J. Experimental Botany47:325-338), and the heat-shock inducible element from the parsleyubiquitin promoter (WO 03/102198). Other stress-inducible promotersinclude rip2 (U.S. Pat. No. 5,332,808 and U.S. Publication No.2003/0217393) and rd29a (Yamaguchi-Shinozaki et al. (1993) Mol. Gen.Genetics 236:331-340). Certain promoters are inducible by wounding,including the Agrobacterium pmas promoter (Guevara-Garcia et al. (1993)Plant J. 4(3):495-505) and the Agrobacterium ORF13 promoter (Hansen etal., (1997) Mol. Gen. Genet. 254(3):337-343). Each of theseaforementioned references are hereby incorporated by reference in theirentireties, particularly as relates to the promoters disclosed withinthe references.

In this disclosure the term “isolated” nucleic acid molecule means anucleic acid molecule that is separated from other nucleic acidmolecules that are usually associated with the isolated nucleic acidmolecule. Thus, an “isolated” nucleic acid molecule includes, withoutlimitation, a nucleic acid molecule that is free of nucleotide sequencesthat naturally flank one or both ends of the nucleic acid in the genomeof the organism from which the isolated nucleic acid is derived (e.g., acDNA or genomic DNA fragment produced by PCR or restriction endonucleasedigestion). Such an isolated nucleic acid molecule is generallyintroduced into a vector (e.g., a cloning vector or an expressionvector) for convenience of manipulation or to generate a fusion nucleicacid molecule. In addition, an isolated nucleic acid molecule caninclude an engineered nucleic acid molecule such as a recombinant or asynthetic nucleic acid molecule. A nucleic acid molecule existing amonghundreds to millions of other nucleic acid molecules within, forexample, a nucleic acid library (e.g., a cDNA or genomic library) or agel (e.g., agarose, or polyacrylamine) containing restriction-digestedgenomic DNA, is not an “isolated” nucleic acid.

The term “nucleic acid” or “polynucleotide” refers to deoxyribonucleicacids (DNA) or ribonucleic acids (RNA) and polymers thereof in eithersingle- or double-stranded form. Unless specifically limited, the termencompasses nucleic acids containing known analogs of naturalnucleotides that have similar binding properties as the referencenucleic acid and are metabolized in a manner similar to naturallyoccurring nucleotides. Unless otherwise indicated, a particular nucleicacid sequence also implicitly encompasses conservatively modifiedvariants thereof (e.g., degenerate codon substitutions), alleles,orthologs, single nucleotide polymorphisms (SNPs), and complementarysequences as well as the sequence explicitly indicated. Specifically,degenerate codon substitutions may be achieved by generating sequencesin which the third position of one or more selected (or all) codons issubstituted with mixed-base and/or deoxyinosine residues (Batzer et al.,Nucleic Acid Res. 19:5081 (1991); Ohtsuka et al., J. Biol. Chem.260:2605-2608 (1985); and Rossolini et al., Mol. Cell. Probes 8:91-98(1994)). The term nucleic acid is used interchangeably with gene, cDNA,and mRNA encoded by a gene.

The term “gene” means the segment of DNA involved in producing apolypeptide chain; it includes regions preceding and following thecoding region (leader and trailer) involved in thetranscription/translation of the gene product and the regulation of thetranscription/translation, as well as intervening sequences (introns)between individual coding segments (exons).

In this application, the terms “polypeptide,” “peptide,” and “protein”are used interchangeably herein to refer to a polymer of amino acidresidues. The terms apply to amino acid polymers in which one or moreamino acid residue is an artificial chemical mimetic of a correspondingnaturally occurring amino acid, as well as to naturally occurring aminoacid polymers and non-naturally occurring amino acid polymers. As usedherein, the terms encompass amino acid chains of any length, includingfull-length proteins (i.e., antigens), wherein the amino acid residuesare linked by covalent peptide bonds.

The term “amino acid” refers to refers to naturally occurring andsynthetic amino acids, as well as amino acid analogs and amino acidmimetics that function in a manner similar to the naturally occurringamino acids. Naturally occurring amino acids are those encoded by thegenetic code, as well as those amino acids that are later modified,e.g., hydroxyproline, .gamma.-carboxyglutamate, and O-phosphoserine. Forthe purposes of this application, amino acid analogs refers to compoundsthat have the same basic chemical structure as a naturally occurringamino acid, i.e., an a carbon that is bound to a hydrogen, a carboxylgroup, an amino group, and an R group, e.g., homoserine, norleucine,methionine sulfoxide, methionine methyl sulfonium. Such analogs havemodified R groups (e.g., norleucine) or modified peptide backbones, butretain the same basic chemical structure as a naturally occurring aminoacid. For the purposes of this application, amino acid mimetics refersto chemical compounds that have a structure that is different from thegeneral chemical structure of an amino acid, but that functions in amanner similar to a naturally occurring amino acid.

Amino acids may include those having non-naturally occurringD-chirality, as disclosed in WO01/12654, which may improve the stability(e.g., half life), bioavailability, and other characteristics of apolypeptide comprising one or more of such D-amino acids. In some cases,one or more, and potentially all of the amino acids of a therapeuticpolypeptide have D-chirality.

Amino acids may be referred to herein by either the commonly known threeletter symbols or by the one-letter symbols recommended by the IUPAC-IUBBiochemical Nomenclature Commission. Nucleotides, likewise, may bereferred to by their commonly accepted single-letter codes.

As used in herein, the terms “identical” or percent “identity,” in thecontext of describing two or more polynucleotide or amino acidsequences, refer to two or more sequences or subsequences that are thesame or have a specified percentage of amino acid residues ornucleotides that are the same (for example, a variant protein used inthe method of this invention has at least 80% sequence identity,preferably 85%, 90%, 91%, 92%, 93, 94%, 95%, 96%, 97%, 98%, 99%, or 100%identity, to a reference sequence), when compared and aligned formaximum correspondence over a comparison window, or designated region asmeasured using one of the following sequence comparison algorithms or bymanual alignment and visual inspection. Such sequences are then said tobe “substantially identical.” With regard to polynucleotide sequences,this definition also refers to the complement of a test sequence.Preferably, the identity exists over a region that is at least about 50amino acids or nucleotides in length, or more preferably over a regionthat is 75-100 amino acids or nucleotides in length.

For sequence comparison, typically one sequence acts as a referencesequence, to which test sequences are compared. When using a sequencecomparison algorithm, test and reference sequences are entered into acomputer, subsequence coordinates are designated, if necessary, andsequence algorithm program parameters are designated. Default programparameters can be used, or alternative parameters can be designated. Thesequence comparison algorithm then calculates the percent sequenceidentities for the test sequences relative to the reference sequence,based on the program parameters. For sequence comparison of nucleicacids and proteins, the BLAST and BLAST 2.0 algorithms and the defaultparameters discussed below are used.

A “comparison window”, as used herein, includes reference to a segmentof any one of the number of contiguous positions selected from the groupconsisting of from 20 to 600, usually about 50 to about 200, moreusually about 100 to about 150 in which a sequence may be compared to areference sequence of the same number of contiguous positions after thetwo sequences are optimally aligned. Methods of alignment of sequencesfor comparison are well-known in the art. Optimal alignment of sequencesfor comparison can be conducted, e.g., by the local homology algorithmof Smith & Waterman, Adv. Appl. Math. 2:482 (1981), by the homologyalignment algorithm of Needleman & Wunsch, J. Mol. Biol. 48:443 (1970),by the search for similarity method of Pearson & Lipman, Proc. Nat'l.Acad. Sci. USA 85:2444 (1988), by computerized implementations of thesealgorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin GeneticsSoftware Package, Genetics Computer Group, 575 Science Dr., Madison,Wis.), or by manual alignment and visual inspection (see, e.g., CurrentProtocols in Molecular Biology (Ausubel et al., eds. 1995 supplement)).

Examples of algorithms that are suitable for determining percentsequence identity and sequence similarity are the BLAST and BLAST 2.0algorithms, which are described in Altschul et al., (1990) J. Mol. Biol.215: 403-410 and Altschul et al. (1977) Nucleic Acids Res. 25:3389-3402, respectively. Software for performing BLAST analyses ispublicly available at the National Center for Biotechnology Informationwebsite, ncbi.nlm.nih.gov. The algorithm involves first identifying highscoring sequence pairs (HSPs) by identifying short words of length inthe query sequence, which either match or satisfy some positive-valuedthreshold score T when aligned with a word of the same length in adatabase sequence. T is referred to as the neighborhood word scorethreshold (Altschul et al., supra). These initial neighborhood word hitsacts as seeds for initiating searches to find longer HSPs containingthem. The word hits are then extended in both directions along eachsequence for as far as the cumulative alignment score can be increased.Cumulative scores are calculated using, for nucleotide sequences, theparameters M (reward score for a pair of matching residues; always >0)and N (penalty score for mismatching residues; always <0). For aminoacid sequences, a scoring matrix is used to calculate the cumulativescore. Extension of the word hits in each direction are halted when: thecumulative alignment score falls off by the quantity X from its maximumachieved value; the cumulative score goes to zero or below, due to theaccumulation of one or more negative-scoring residue alignments; or theend of either sequence is reached. The BLAST algorithm parameters W, T,and X determine the sensitivity and speed of the alignment. The BLASTNprogram (for nucleotide sequences) uses as defaults a word size (W) of28, an expectation (E) of 10, M=1, N=-2, and a comparison of bothstrands. For amino acid sequences, the BLASTP program uses as defaults aword size (W) of 3, an expectation (E) of 10, and the BLOSUM62 scoringmatrix (see Henikoff and Henikoff, Proc. Natl. Acad. Sci. USA 89:10915(1989)).

The BLAST algorithm also performs a statistical analysis of thesimilarity between two sequences (see, e.g., Karlin and Altschul, Proc.Nat'l. Acad. Sci. USA 90:5873-5787 (1993)). One measure of similarityprovided by the BLAST algorithm is the smallest sum probability (P(N)),which provides an indication of the probability by which a match betweentwo nucleotide or amino acid sequences would occur by chance. Forexample, a nucleic acid is considered similar to a reference sequence ifthe smallest sum probability in a comparison of the test nucleic acid tothe reference nucleic acid is less than about 0.2, more preferably lessthan about 0.01, and most preferably less than about 0.001.

An indication that two nucleic acid sequences or polypeptides aresubstantially identical is that the polypeptide encoded by the firstnucleic acid is immunologically cross reactive with the antibodiesraised against the polypeptide encoded by the second nucleic acid, asdescribed below. Thus, a polypeptide is typically substantiallyidentical to a second polypeptide, for example, where the two peptidesdiffer only by conservative substitutions. Another indication that twonucleic acid sequences are substantially identical is that the twomolecules or their complements hybridize to each other under stringentconditions, as described below. Yet another indication that two nucleicacid sequences are substantially identical is that the same primers canbe used to amplify the sequence.

In this disclosure the terms “stringent hybridization conditions” and“high stringency” refer to conditions under which a probe will hybridizeto its target subsequence, typically in a complex mixture of nucleicacids, but to no other sequences. Stringent conditions aresequence-dependent and will be different in different circumstances.Longer sequences hybridize specifically at higher temperatures. Anextensive guide to the hybridization of nucleic acids is found inTijssen, Techniques in Biochemistry and Molecular Biology—Hybridizationwith Nucleic Probes, “Overview of principles of hybridization and thestrategy of nucleic acid assays” (1993) and will be readily understoodby those skilled in the art. Generally, stringent conditions areselected to be about 5-10° C. lower than the thermal melting point(T_(m)) for the specific sequence at a defined ionic strength pH. TheT_(m) is the temperature (under defined ionic strength, pH, and nucleicconcentration) at which 50% of the probes complementary to the targethybridize to the target sequence at equilibrium (as the target sequencesare present in excess, at T_(m), 50% of the probes are occupied atequilibrium). Stringent conditions may also be achieved with theaddition of destabilizing agents such as formamide. For selective orspecific hybridization, a positive signal is at least two timesbackground, preferably 10 times background hybridization. Exemplarystringent hybridization conditions can be as following: 50% formamide,5×SSC, and 1% SDS, incubating at 42° C., or, 5×SSC, 1% SDS, incubatingat 65° C., with wash in 0.2×SSC, and 0.1% SDS at 65° C.

Nucleic acids that do not hybridize to each other under stringentconditions are still substantially identical if the polypeptides whichthey encode are substantially identical. This occurs, for example, whena copy of a nucleic acid is created using the maximum codon degeneracypermitted by the genetic code. In such cases, the nucleic acidstypically hybridize under moderately stringent hybridization conditions.Exemplary “moderately stringent hybridization conditions” include ahybridization in a buffer of 40% formamide, 1 M NaCl, 1% SDS at 37° C.,and a wash in 1×SSC at 45° C. A positive hybridization is at least twicebackground. Those of ordinary skill will readily recognize thatalternative hybridization and wash conditions can be utilized to provideconditions of similar stringency. Additional guidelines for determininghybridization parameters are provided in numerous references, e.g.,Current Protocols in Molecular Biology, ed. Ausubel, et al.

The soybean line selected for mapping can be subjected to DNAextraction. In embodiments of the present invention, the CTAB method(Murray and Thompson, Nucl. Acids Rev. 8:4321-4325, 1980; Keim et al.,Soybean Genet. Newsl. 15:150-152, 1988) can be used. Nucleic acid probescan be used as markers in mapping the resistance loci, and appropriateprobes can be selected based upon the mapping method to be used. Theprobes can be either RNA or DNA probes, and mapping can be performedusing a number of methods recognized in the art, including, for example,AFLP, RFLP, RAPD, or microsatellite technology. Additionally, globalgene expression profiling using microarrays has been extensivelyinvestigated during plant-nematode interactions.

In some embodiments of the present invention, DNA probes can be used forRFLP markers. Such probes can come from, for example, Pst I-clonedgenomic libraries, and the cloned inserts used as probes may beamplified, for example by PCR, LCR, NASBA™, or other amplificationmethods recognized in the art. For example, the markers useful in apreferred embodiment of the invention include the following: pA85a,php02302a, php02340a, pK400a, pT155a, pBLT24a, pBLT65a, php05180a,pSAC3a, pA1116, php05266a, php022986, pA664a, pA63a, php02366a,php02361a, php05354a, php05219a, pK69a, pL50c, pK18a, pA567a, pA407a,pA4046, pA226a, pA715a, pK24a, pB157b, php02275a, php05278a, php05240c,pBLT49a, pK79a, and php03488a. FIG. 1 shows the linkage groups withwhich the foregoing probes are associated. The Pioneer Hi-BredInternational, Inc. proprietary nucleic acid markers have been depositedwith the ATCC and are available as follows: php05354 assigned ATCC98495; php05219 assigned ATCC 98490; php02366 assigned ATCC 69934;php02340 assigned ATCC 69935; php02361 assigned ATCC 69936; php02301assigned ATCC 69937; php05180 assigned ATCC 69938; php02275 assignedATCC 69937; and php02302 assigned ATCC 69940. The other, non-proprietaryprobes are available from Linkage Genetics, Salt Lake City, Utah, andfrom Biogenetic Services, Brookings, S. Dak.

For RFLP mapping, restriction fragments can be generated using specificrestriction enzymes, and the digestion, electrophoresis, Southerntransfers and nucleic acid hybridizations are conducted according toart-recognized techniques. See, e.g., Keim et al., Theor. Appl. Genet.77:786-792, 1989, the disclosure of which are hereby incorporated hereinby reference.

In alternative embodiments of the present invention, RAPD technology canbe utilized for genetic mapping. A DNA preparation can be amplifiedusing art-recognized amplification techniques, and suitable nucleic acidmarkers are used. Alternatively, other genetic mapping technologiesrecognized in the art can be used in the practice of the presentinvention.

In a soybean breeding program, the method of the present inventionenvisions the use of marker-associated selection for one or more loci atany stage of population development in a two-parent population, multipleparent population, or a backcross population. Such populations aredescribed in Fehr, W. R. 1987, Breeding Methods for CultivarDevelopment, in J. R. Wildox (ed.) Soybeans: Improvement, Production,and Uses, 2d Ed., the disclosures of which are hereby incorporatedherein by reference.

Marker-assisted selection according to art-recognized methods can bemade, for example, step-wise, whereby the different SCN resistance lociare selected in more than one generation; or, as an alternative example,simultaneously, whereby all three loci are selected in the samegeneration. Marker-assisted selection for SCN resistance can be donebefore, in conjunction with, or after testing and selection for othertraits such as seed yield.

The DNA from target populations can also be obtained from any plantpart, and each DNA sample may represent the genotype of single ormultiple plant individuals (including seed).

Marker-assisted selection can also be used to confirm previous selectionfor SCN resistance or susceptibility made by challenging plants withsoybean cyst nematodes in the field or greenhouse and scoring theresulting phenotypes.

The following examples offered by way of illustration and not by way oflimitation.

Example 1

In order to profile the DNA methylation patterns at single nucleotideresolution during the susceptible interaction with SCN, six whole genomebisulfite-treated DNA libraries were constructed. In these experiments,soybean cultivar Williams 82 was inoculated with SCN (race 3) and roottissues were collected at 4 day post inoculation (dpi) from bothinfected and non-infected soybean roots, from three independentexperiments. Three libraries from each infected and non-infected sampleswere generated and sequenced using the Illumina HiSeq platform. Thesequencing data were grouped into six different files and a total numberof 175 million 100 bp reads for SCN-infected samples and 182 millionreads for non-infected control were obtained. After quality filtering atotal of about 88 and 92 million reads for SCN-infected and non-infectedsamples respectively, were of high quality and uniquely mapped tosoybean genome (Wm82.a2.v1) (Table 1).

TABLE 1 Summary of cytosine methylation in control and SCN-infectedsamples Control SCN-Infected Total number of high quality reads91,560,375 87,972,505 analyzed Number of reads with unique hits59,900,029 59,875,941 Mapping efficiency 65.40% 68.06% Conversion % 99.6%  99.6% Total number of C's analyzed 1,874,012,046 1,792,959,026 %methylated C's in CpG context 81.00% 78.60% % methylated C's in CHGcontext 59.30% 56.40% % methylated C's in CHH context  5.50%    5%

These high quality sequence reads represent more than 10× genomecoverage, a depth greater than which was previously reported inArabidopsis and soybean (Dowen et al., 2012; Schmitz et al., 2013).Bisulfite conversion efficiency was higher than 99% as determined usingthe non-methylated lambda phage genome. The percentage of methylatedcytosine (mC) in CpG, CHG and

CHH contexts were very similar across all the biological replicates forSCN-infected and non-infected control. The SCN-infected samples had anaverage of 78.6%, 56.4% and 5.0% methylation overall mC in CpG, CHG andCHH contexts, respectively (Table 1). Similarly, the control samples hadan average of 81%, 59.3% and 5.5% methylation overall mC in CpG, CHG andCHH contexts, respectively (Table 1). These data indicate that overallaverage methylation levels are very similar between the SCN-infected andcontrol samples.

Example 2

The methylome of SCN-infected and control roots were compared toidentify differentially methylated regions. Differentially hyper- andhypo-methylated regions (200 bp bin) in CpG, CHG and CHH contexts wereidentified using P-value <0.01 and percent methylation difference largerthan 25%. 718 hyper-methylated regions and 1408 hypo-methylated regionswere identified in the infected roots compared with the non-infectedcontrol in CpG (FIG. 1, Supplemental Table 1 and 2). 1142hyper-methylated regions and 2074 hypo-methylated regions wereidentified in CHG (FIG. 1, Supplemental Table 3 and 4). 605hyper-methylated regions and 1210 hypo-methylated regions wereidentified in CHH (FIG. 1, Supplemental Table 5 and 6). These resultsdemonstrate that SCN induces hypo-methylation to much higher extentcompared to hyper-methylation.

Example 3

Gene overlapping was determined by comparing the hyper-methylated genes.Approximately 60% (429 genes), 16% (180 genes), and 20% (120 genes) ofthe hyper-methylated regions in CpG, CHG and CHH contexts, respectively,overlapped with protein-coding genes.

Similarly, 58% (818 genes), 17% (350 genes), and 23% (282 genes) of thehypo-methylated regions in CpG, CHG and CHH contexts, respectivelyoverlapped with protein-coding genes. As a result, a total number of 703and 1346 unique genes were identified as hyper- and hypo-methylated,respectively (Supplemental Table 7 and 8). Methylation contexts occur inindividual genes was next examined. Such examination found that 25 genesthat were hyper-methylated in more than one context in which 6 geneswere found to be hyper methylated in both CHH and CHH contexts, 6 genesin CHH and CpG and 13 genes in CpG and CHG contexts (FIG. 2A andSupplemental Table 7). Also, 101 genes that were hypo-methylated in morethan one context were identified (FIG. 2B and Supplemental Table 8).

The hyper- and hypo-methylation in CpG and CHG contexts occurpredominantly in the gene body and to much less extent in the flankingregions, including promoter, 5′ and 3′ untranslated regions (UTR) (FIG.3A and B). In contrast, CHH hyper-methylation was mainly located in thepromoter regions, 1000 bp upstream of the transcription start site(TSS). A set of 45 genes showed both hyper- and hypo-methylation invarious genic and promoter regions

The DMR-associated genes into different groups by molecular function andassociated biological processes using the Gene Ontology (GO)categorization from SoyBase (www.soybase.org). Molecular function groupswere found to correspond to binding activity, catalytic activity,transferase activity and hydrolase activity (FIG. 4A). When these geneswere grouped by associated biological processes a significant portion ofgenes was found to be associated with signal transduction, carbohydratemetabolic process, transport, cell growth, and translation (FIG. 4B). GOterm enrichment analysis revealed that genes associated with genesilencing, organ morphogenesis and actin nucleation are overrepresented.

Example 4

It was further determined that the overlap with the syncytiumdifferentially expressed genes. The differentially hyper- andhypo-methylated genes identified were compared with a reference list ofgenes that changes the expression in the syncytium induced by SCN (6962genes). 70, 16 and 13 genes of differentially hyper-methylated genes inCpG, CHG and CHH contexts, were determined to respectively overlap withsyncytial differentially expressed genes (FIG. 5A). Similarly, 123, 30and 44 genes of differentially hypo-methylated genes in CpG, CHG and CHHcontexts, respectively were found to overlap with syncytialdifferentially expressed genes (FIG. 5B). After eliminating duplicatedgenes that are differentially methylated in more than one context, 93genes were identified of the differentially hyper-methylated genes and193 of the differentially hypo-methylated genes as overlapping with the6962 syncytium-regulated genes (Supplemental Table 9 and 10). A set of 8genes were found to be both hyper-and hypomethylated in different genicregions.

These 278 genes represent only 4% of the total number ofsyncytium-regulated genes. When these genes were classified by molecularfunction and associated biological processes using GO categorization,the binding activity and catalytic activity were determined to be themost abundant molecular functions of these genes (FIG. 5C), whereastranslation, signal transduction, carbohydrate metabolic process andtransport are the most abundant associated biological processes (FIG.5D).

Example 5

Next the impact of DNA methylation in the gene body and promoter regionson the gene expression levels was tested. RNA was isolated from the sameSCN-infected and control samples and used in quantitative real-timeRT-PCR (qPCR) assays. An association between gene body hyper-methylationin various contexts and both increased and decreased gene expressionlevels (FIG. 6A), whereas hypo-methylation gene body was found to becorrelated with increased levels of gene expression (FIG. 6B). The studyalso demonstrated that increased CpG, CHG and CHH methylation in thepromoter regions was negatively correlated with gene expression levels,whereas demethylation was positively correlated with gene expressionlevels (FIG. 6C and D). This illustrates that the differentialmethylation in gene bodies and promoters contributes to gene expressionregulation.

Example 6

An examination also determined whether differential cytosine methylationoccurs in miRNA genes in response to SCN infection. Three miRNA genes(miR169s, miR394 and miR5036) were identified as hypermethylated at thepromoter region (1 KB upstream of TSS site) in CHH or CpG contexts(Table 2).

TABLE 2 List of 37 miRNA genes that are differentially methylated inresponse to SCN infection. The sequences of the miRNA can be found inthe sequence listing or at mirbase.org. Differentially Methylated RegionContext Gend ID Description Gene feature Chr01.2409001-2410000 Hypo_CpGMI0016507 gma-miR4367 promoter Chr01.42333001-42334000 Hypo_CHGMI0017845 gma-miR390c promoter Chr01.49102001-49103000 Hypo_CHH,MI0017838 gma-miR171d promoter CHG Chr01.7196001-7197000 Hypo_CHGMI0001787 gma-miR398a promoter Chr02.14637001-14638000 Hypo_CpGMI0001778 gma-miR167b promoter Chr03.2852001-2853000 Hypo_CpG MI0031032gma-miR9746e promoter Chr03.2871001-2872000 Hyper_CHG MI0031033gma-miR9746f promoter Chr04.12841001-12842000 Hypo_CHG MI0007237gma-miR1522 promoter Chr04.46346001-46347000 Hypo_CpG MI0018674gma-miR319i promoter Chr06.11435001-11436000 Hypo_CHG, MI0031039gma-miR319o promoter CPG Chr06.11979001-11980000 hyper_CpG MI0016470gma-miR4341 promoter Chr06.1502001-1503000 hyper_CpG, MI0021713gma-miR394g miRNA primary CHG transcript & promoterChr06.47265001-47266000 hyper_CpG MI0019728 gma-miR5778 promoterChr07.11671001-11672000 Hypo_CpG MI0016511 gma-miR4369 promoterChr07.11672001-11673000 hyper_CpG MI0016511 gma-miR4369 promoterChr07.1365001-1366000 hyper_CpG MI0016539 gma-miR4386 promoterChr07.1503001-1504000 Hypo_CHH MI0016526 gma-miR4379 promoterChr07.19892001-19893000 Hypo_CHG MI0010576 gma-miR2107 promoterChr08.1770001-1771000 hyper_CpG MI0017909 gma-miR5036 promoterChr08.4639001-4640000 Hypo_CpG MI0018645 gma-miR397a miRNA primarytranscript & promoter Chr08.46830001-46831000 Hypo_CpG MI0019267gma-miR5037d promoter Chr09.28529001-28530000 Hypo_CHG MI0017855gma-miR1508c promoter Chr10.31594001-31595000 Hypo_CHG MI0018668gma-miR172g promoter Chr11.29820001-29821000 hyper_CpG, MI0018622gma-miR5369 promoter CHG Chr11.33759001-33760000 hyper_CpG, MI0016512gma-miR4370 promoter CHG Chr11.9033001-9034000 Hypo_CpG MI0019740gma-miR828a miRNA primary transcript & promoter Chr13.37640001-37641000Hyper_CHG MI0031006 gma-miR4348b promoter Chr16.29727001-29728000Hypo_CpG MI0031009 gma-miR9729 promoter Chr17.1497001-1498000 hyper_CHHMI0007227 gma-miR1514b miRNA primary transcript & promoterChr17.6626001-6627000 hyper_CpG MI0016518 gma-miR4373 promoterChr18.3402001-3403000 Hypo_CHG MI0016552 gma-miR4396 miRNA primarytranscript & promoter Chr18.35312001-35313000 hyper_CpG MI0010576gma-miR2107 promoter Chr19.1919001-1920000 Hypo_CpG MI0019714gma-miR5225 promoter Chr19.47164001-47165000 hyper_CpG, MI0017848gma-miR408d promoter CHG Chr20.35349001-35350000 Hypo_CpG MI0017849gma-miR2118a miRNA primary transcript & promoter Chr20.37903001-37904000hyper_CpG MI0017926 gma-miR167i promoter Chr20.40357001-40358000hyper_CpG MI0007250 gma-miR1531 miRNA primary transcript &promoter

TABLE 2A Differentially methylated region overlapping with miRNA genesDifferentially methylated region Context Gene ID Description GeneFeature Chr04.1509401-1509600 Hyper CHH MI0017846 gma-miR394c PromoterChr08.1770401-1770600 Hyper CpG MI0017909 gma-gma-miR5036 PromoterChr17.4864201-4864400 Hyper CHH MI0019763 gma-miR169S Promoter, Primarytranscript Chr01.2409601-2409800 Hypo CpG MI0016507 gma-miR4367 PromoterChr03.5293001-5293200 Hypo CHH MI0017827 gma-miR164c Promoter

In addition, miR164 and miR4367 were identified as demethylated at thepromoter region in CHH and CpG contexts, respectively (Table 2).

While the foregoing instrumentalities have been described in some detailfor purposes of clarity and understanding, it will be clear to oneskilled in the art from a reading of this disclosure that variouschanges in form and detail can be made without departing from the truescope of the invention. For example, all the techniques and apparatusdescribed above may be used in various combinations. All publications,patents, patent applications, or other documents cited in thisapplication are incorporated by reference in their entirety for allpurposes to the same extent as if each individual publication, patent,patent application, or other document were individually indicated to beincorporated by reference for all purposes.

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Sequences of the genes identified by the Glyma IDs provided inSupplemental Tables 7-10 can be found in the soybase.org database andthe sequences associated with the Glyma IDs within the Soybase.orgdatabase are hereby incorporated by reference in their entireties.

LENGTHY TABLES The patent application contains a lengthy table section.A copy of the table is available in electronic form from the USPTO website(http://seqdata.uspto.gov/?pageRequest=docDetail&DocID=US20170369900A1).An electronic copy of the table will also be available from the USPTOupon request and payment of the fee set forth in 37 CFR 1.19(b)(3).

1-35. (canceled)
 36. An elite soybean plant, or a part thereof,comprising one or more introgressed Soybean Cyst Nematode (SCN)resistance loci, wherein said elite soybean plant comprises one or moreagronomic traits selected from the group consisting of herbicidetolerance, increased yield, insect control, fungal disease resistance,virus resistance, nematode resistance, bacterial disease resistance,mycoplasma disease resistance, modified oils production, high oilproduction, high protein production, germination and seedling growthcontrol, enhanced animal and human nutrition, lower raffinose,environmental stress resistance, increased digestibility, production ofindustrial enzymes, production of pharmaceutical proteins, production ofpharmaceutical peptides, production of pharmaceutical small molecules,improved processing traits, improved flavor, improved nitrogen fixation,improved hybrid seed production, reduced allergenicity, and improvedproduction of biopolymers and biofuels.
 37. The elite soybean plant, ora part thereof, of claim 36, wherein said elite soybean plant isresistant to Heterodera glycines.
 38. The elite soybean plant, or a partthereof, of claim 36, wherein said elite soybean plant comprises one ormore traits selected from the group consisting of insect resistance,glyphosate resistance, resistance to Asian Soybean Rust, resistance toMeloidogyne javanica, resistance to Meloidogyne arenaria, resistance toMeloidogyne hapla, resistance to Meloidogyne incognita, resistance toDiaporthe phaseolorum var. caulivora, and resistance to Corynesporacassiicola.
 39. The elite soybean plant, or a part thereof, of claim 36,wherein said part is selected from the group consisting of a seed,endosperm, an ovule, and a pollen.
 40. The elite soybean plant, or apart thereof, of claim 36, wherein said elite soybean plant istransgenic.
 41. The elite soybean plant, or part thereof, or claim 36,wherein said elite soybean plant comprises one or more heterologousnucleic acid sequences encoding one or more miRNA selected from SEQ IDNOs: 1-37 or one or more nucleic acid sequences encoding one or moremiRNA selected from SEQ ID NOs: 1-37 operably linked to a heterologouspromoter.
 42. The elite soybean plant, or part thereof, of claim 36,wherein said elite soybean plant comprises one or more heterologousnucleic acid sequences encoding one or more gene selected from SEQ IDNOs: 38-315 or one or more construct comprising any one of SEQ ID NOs:38-315 operably linked to a heterologous promoter.
 43. The elite soybeanplant, or part thereof, of claim 36, wherein said elite soybean plantcomprises one or more heterologous nucleic acid sequences encoding oneor more miRNA selected from SEQ ID NOs: 1-37 and one or moreheterologous nucleic acid sequences encoding one or more gene selectedfrom SEQ ID NOs: 38-315 or one or more heterologous promoter operablylinked to a nucleic acid sequence encoding one or more miRNA selectedfrom SEQ ID NOs: 1-37 and one or more heterologous promoter operablylinked to a nucleic acid sequence encoding one or more gene selectedfrom SEQ ID NOs: 38-315.
 44. A method for producing an SCN resistantsoybean plant comprising: a performing marker assisted selection toidentify a soybean plant possessing a resistance allele of SCNresistance locus, wherein the SCN resistance locus is identifiable byone or more of the markers and generating a progeny of said soybeanplant wherein said progeny possesses said resistance allele of SCNresistance locus and exhibits at least partial resistance to SCN. 45.The method of claim 44, said method produces an SCN resistant elitesoybean plant.
 46. The method of claim 44, wherein said marker assistedselection is conducted using an assay selected from the group consistingof single base extension (SBE), allele-specific primer extensionsequencing (ASPE), DNA sequencing, RNA sequencing, microarray-basedanalyses, universal PCR, allele specific extension, hybridization, massspectrometry, ligation, extension-ligation, and FlapEndonuclease-mediated assays.
 47. The method of claim 44, wherein saidsoybean plant produced by said method further comprises one or moretraits selected from the group consisting of herbicide tolerance,increased yield, insect control, fungal disease resistance, virusresistance, nematode resistance, bacterial disease resistance,mycoplasma disease resistance, modified oils production, high oilproduction, high protein production, germination and seedling growthcontrol, enhanced animal and human nutrition, lower raffinose,environmental stress resistance, increased digestibility, improvedprocessing traits, improved flavor, improved nitrogen fixation, improvedhybrid seed production, reduced allergenicity, and improved productionof biofuels.
 48. The method of claim 44, wherein said soybean plantproduced by said method is resistant to a herbicide selected from thegroup consisting of glyphosate, dicamba, glufosinate, sulfonylurea,bromoxynil, 2,4-Dichlorophenoxyacetic acid, and norflurazon.
 49. Themethod of claim 44, wherein said soybean plant produced by said methodis transgenic.
 50. A method for generating a soybean plant, said methodcomprising (a) introgressing SCN resistance into an SCN sensitivesoybean germplasm, (b) determining the presence or absence of a markergene or a fragment thereof and a transgene, and (c) allowing thegermplasm generated in (a) to develop into a soybean plant resistant tosoybean cyst nematode (SCN) if the marker and transgene are present,wherein step (a) precedes step (b).
 51. The method of claim 50, whereinthe transgene is selected from nucleic acid sequences encoding one ormore miRNA selected from SEQ ID NOs: 1-37 and/or one or more nucleicacid sequences encoding one or more gene selected from SEQ ID NOs:38-315.
 52. The method of claim 50, wherein the soybean plant isintrogressed with nucleic acid sequences encoding one or more miRNAselected from SEQ ID NOs: 1-37 and/or one or more nucleic acid sequencesencoding one or more gene selected from SEQ ID NOs: 38-315.